This information is for Vicon Nexus 2.8. For up-to-date help, see the latest Nexus documentation.

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The Pipeline Tools pane enables you to create and manage a customized sequence of operations to automate the processing of a trial.

Pipeline processing is optional, but is useful for automating the data processing operations that you use frequently or on a large number of trials.

The Pipeline Tools pane contains the following sections:

  • Available Operations section

    The Available Operations section enables you to select the type of pipeline you want to create and the operations to run. Operations are grouped under the following types:

  • Current Pipeline section
    At the top of the Current Pipeline section, the configuration management controls enable you to create or manage configurations for the settings specified in the Pipeline Tools pane.

    The middle of the Current Pipeline section enables you to manage the pipeline operations and view their status with the playback controls and progress bar.

    In the list at the bottom of the Current Pipeline section, you can view the operations included in the currently loaded pipeline.

    For information on using pipelines, see Work with pipelines in the Vicon Nexus User Guide.

    Tip

    Pipeline operations are run in the order they appear in this list. You can drag operations into the desired position in the list. Alternatively, you can run an individual operation by right-clicking on it and clicking Run selected Op.

  • Properties pane
    You can view or change settings for the selected pipeline operation in the Properties pane at the bottom of the Pipeline Tools pane.

Pipeline operations

Pipeline operations are found in the Pipeline Tools pane, in the Available Operations section.

File Import operations

Use File Import operations to automate the import of trial files to Vicon Nexus from third-party software packages.

Operation

Description

Import AVI

Import a video .avi file to be saved and associated with the current trial.

Import MP

Import subject parameters specified in a .mp file into the active subject.

Import VSK

Import a labeling skeleton (.vsk) file.

Import XCP

Import a calibration file (.xcp) into the current trial to replace the current calibration.

Core Processing operations

Use Core Processing operations to automate the processing of offline reconstruction, labeling, and kinematic fitting to produce 3D trajectories from raw marker data.

Operation

Description

Combined Processing

Performs one or more of: reconstruction, labeling, and subject motions. Running this operation is faster than running each process individually.

Reconstruct

3D trajectories are reconstructed from the raw 2D marker data.

Label

Controls how 3D trajectories are labeled with subject data

Kinematic Fit

Controls how the labeling skeleton contained in the .vsk is kinematic-fitted to the marker data. In addition to specifying the frames on which to operate, you can adjust settings for:

  • Prior importance: Weighting given to the uncalibrated values from the VST. Range is 0-100, default is 25.
  • Mean pose ratio: Ratio of tracking pose as prior (where 0 = mean pose only; 1 (default) = external (or tracking) prior only.)

The equivalent settings for Live processing can be found in the Local Vicon System properties, found in the System Resources pane.

Subject Calibration operations

Use Subject Calibration operations to automate the processing of labeling skeleton calibration.

Operation

Description

Set Autolabel Pose

Sets the pose for Autolabel Static to be the pose at the selected frame.

Autolabel Static

Run on a reconstructed static trial to automatically label the labeling skeleton in a single frame, using information from the .vst file. It matches the shape of the reconstruction to the shape of the subject template for that pose.
The labels are applied to the whole trajectory, not just the chosen frame. It works best when all the markers have been reconstructed and there are no additional markers or clutter in the scene.
This operation does not require a .vsk file. 

Scale Subject VSK

Scales the labeling skeleton to be the same size as a labeled set of reconstructions on a particular frame. The scale factor is calculated assuming that the subject is in the same pose as was used for Autolabel Static (see above).
(Note that this scaling respects any constraints that you may have specified in the template. For example if your template specifies (ie a StaticParameter) that a segment is 100mm long, the segment will not be scaled. Only parameters are considered for scaling.)

Functional Skeleton Calibration

Calibrate the subject's bone lengths, joint locations, and marker locations from a whole trial. Use to calibrate a whole ROM trial.

Functional Skeleton Calibration - Markers-only

Calibrate the subject's marker locations from a whole trial. This is useful, for example if a marker becomes detached from the subject and you need to re-run the calibration with the replaced marker.

Static Skeleton Calibration

Calibrate the subject's bone lengths, joint locations, and marker locations from a single frame. Use to calibration a static calibration, as in versions of Vicon Nexus earlier than 2.0.

Static Skeleton Calibration - Markers-only

Uses a single frame to update the marker locations for the labeling skeleton. This operation both fits the subject pose (that is, the pose that was defined when the labeling skeleton was created) to the labeled reconstructions and calibrates the marker locations.
Fitting the subject pose allows for the likely situation of your subject standing close to the template pose. Again, this operation respects any constraints specified in the labeling skeleton template and changes only parameters.
This operation is useful, for example if a marker becomes detached from the subject and you need to re-run the calibration with the replaced marker.

Update Skeleton Parameters

Initial label booting can be improved by providing more representative data from a movement or ROM trial. This operation enables you to do this by updating the default values of a selected skeleton with movement or ROM trial data contained in the current calibrated labeling skeleton (VSK). The options for this operation are:

  • Update Marker Covariances Marker covariance is used by the labeler to account for skin motion, so the default for this option is Selected.
  • Update Parameters If you have calibrated a skeleton from the Labeling Template Builder, select this check box.
  • Update Joint Mean & Covariance Joint covariance is used in booting the labeling. If you have a very flexible subject, a larger covariance will help, so select this check box.
  • Update Joint Ranges Joint ranges can be enforced to detect infeasible joint angles. If you have a very flexible subject, larger joint ranges are needed, so select this check box.

Calculate Skeleton Joint & Marker Statistics

Measure the subject's labeling statistics from a whole trial.

Calibrate OCST

Finds the Optimum Common Shape

Calibrate SCoRE/SARA

Calibrate joint positions using the Symmetrical Center of Rotation Estimation and Symmetrical Axis of Rotation Analysis.

For more information on the labeling skeleton calibration operations, see Labeling skeleton calibration in detail.

Events & Timebar operations

Use Events & Timebar operations to automate processes relating to events and the timebar.

Operation

Description

Auto Crop Trial

For trials where the subject starts outside the volume, moves into the volume and then exits, Nexus can automatically determine the first and last frame where the subject is fully in the volume.

  • First Frame and Last Frame Set these options to the frames during which the subject enters and leaves the volume.
  • Start % and End % Set these options to the required minimum percentage of markers (ie, the percentage expected from the total number of markers in your subject's labeling skeleton) that must be labeled in each case.
  • Frames Required If necessary, adjust this option to set a minimum number of frames where the Start % criterion must be met. This is helpful if early single frames of data meet the percentage, but the point at which the trial is intended to start (ie, the point at which the percentage is maintained over a number of frames) is later in the trial.

Autocorrelate Events

Based on user-defined parameters, this operation detects the pattern of the tracked marker at the set events and defines these events for the rest of the trial. The available parameters are: marker being tracked; the X, Y, or Z component of the marker; and the position, velocity, or acceleration of the marker. Normally used after the Detect Events from Forceplate operation.

Detect Events from ForcePlate

Automatically detects gait cycle events and adds them to the time bar throughout the trial using vertical GRFs measured by a force plate connected to the Vicon system. Includes the option to set the force threshold and the label of the markers attached to the front and back of the foot for both sides.

Delete Timebar Events

Delete events from the specified range for the subject(s). An advanced option lets you choose whether to delete events that are inside or outside the specified range of frames.

Fill Gap & Filter Data operations

Use Fill Gap & Filter Data operations to automate gap-filling and other post-processing.

Operation

Description

Fill Gaps - Cyclic

For trials that contain captured data that is cyclic in nature (for example, when a motion on a treadmill or other repetitive motion is captured), fills gaps using patterns from earlier or later gait cycles. You can specify the Gap Length, Units, First and Last Frame, and select the trajectories to fill.

Fill Gaps - Kinematic

Fills all gaps in trajectories that pass through a selected segment, based on calculated kinematics. To run this operation, you must have already obtained the kinematic data on which to base gap-filling, for example, by running the Nexus Legacy Fit Motion pipeline.

Fill Gaps - Pattern

Fills the selected gap using the shape of another trajectory without a gap. Use this tool only if there is a suitable marker with a trajectory similar to the one whose gap you wish to fill.

Fill Gaps - Rigid Body

Fills gaps in a trajectory based on other trajectories in a rigid body. This option is the Nexus equivalent of the Replace 4 option, which is available in BodyBuilder. Use this option when a rigid or semi-rigid relationship exists between markers.

Fill Gaps - Woltring

Run on labeled dynamic trials to fill in gaps using Woltring quintic spline interpolation. Includes the option to choose maximum gap frame length to fill.

You can configure the following settings in the Properties section:

  • Max Gap Length The maximum length of any gap in a marker trajectory that will be filled with this operation.
    Default: 5
  • First Frame The first of the range of frames in the region of interest of the trial that you wish to analyze. For example, if the capture includes the subject entering the capture volume, you are strongly advised to set the range of frames to exclude this portion of the capture. That will simplify the job of cleaning up your data. You can specify the following settings:
    • First Frame: The first frame of the trial.
    • Selected Start: The frame indicated by the Start Range Frame indicator on the time bar ruler.
    • Current Frame: The frame indicated by the Current Time indicator on the time bar ruler.
    • First Full Frame: First full frame of range to process
      Default: Selected Start
  • Last Frame The last of the range of frames in the region of interest of the trial that you wish to analyze. For example, if the capture includes the subject leaving the capture volume, you are strongly advised to set the range of frames to exclude this portion of the capture. That will simplify the job of cleaning up your data. You can specify the following settings:
    • End Frame: The last frame of the trial.
    • Selected End: The frame indicated by the End Range Frame indicator on the time bar ruler.
    • Current Frame: The frame indicated by the Current Time indicator on the time bar ruler.
    • Last Full Frame: Last full frame of range
      Default: Selected End

Filter Analog Data - Butterworth

Filter analog device data using a low-pass digital Butterworth filter. The filter is by default setup as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 300 Hz using a fourth order filter with zero lag (see descriptions below for an explanation of these parameters).
Note: For force plates, only the calculated Force and Moment signals can be filtered. Raw and Center of Pressure signals cannot be filtered.
You can configure the following settings in the Properties section:

  • Cut-Off Frequency The filter cut-off frequency, separating the low-frequency signal from high frequency noise. Data at frequencies above the cut-off frequency are attenuated increasingly as the frequency increases. The attenuation exactly at the cut-off frequency is designed to be "half power," or -3 dB. Note Cut-off frequencies greater than half of the analog device sampling frequency (often called the Nyquist frequency) cannot be used and will result in an error message and no filtering of the data.
  • Filter Order The Second Order filter performs a single pass of the filter in the forwards (increasing time) direction, resulting in a "lag," or "phase shift" in the analog data. The Fourth Order filter performs two passes of the filter, in first the forward, then the reverse direction, resulting in any lag being cancelled out (hence "zero lag"). The parameters of the Fourth Order filter are adjusted, such that the attenuation exactly at the cut-off frequency is maintained at "half power," or -3 dB.
  • Filter Type Can be Low Pass (the default) or High Pass. Select High Pass to filter low-frequency noise from your data.
  • Devices A comma separated list of Devices, Outputs and Components can be typed, or the Macros All or Selected can be used. All will always filter the data from every device currently connected and Selected will filter the data from the devices, device outputs, and output components with names matching those currently selected in the System resource pane and in the 3D Perspective view.

Filter Model Outputs - Butterworth

Filter subject model outputs using a low-pass digital Butterworth filter. The filter is by default setup as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 6 Hz using a Fourth Order filter with zero lag.
You can configure the following settings in the Properties section:

  • Cut-Off Frequency Same as Analog Data above.
  • Filter Order Same as Analog Data above.
  • Model Outputs A comma separated list of Model Outputs can be typed, or the Macros All or Selected can be used. All will always filter all Model Outputs calculated for a subject and Selected will filter Model Outputs with names matching those currently selected on the Subjects tab of the Resources pane and in the 3D Perspective view. You can use the * wildcard for all model outputs.

Filter Trajectories - Butterworth

Filter trajectories using a low-pass digital Butterworth filter. The filter is by default set up as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 6 Hz using a Fourth Order filter with zero lag.
You can configure the following settings in the Properties section:

  • Cut-Off Frequency Same as Analog Data above.
  • Filter Order Same as Analog Data above.
  • Trajectories A comma separated list of trajectories can be typed, or the Macros All, All Labeled, or Selected can be used. All will always filter every trajectory, including unlabeled ones, All Selected will filter every currently labelled trajectory, and Selected will filter trajectories with names matching those labelled trajectories currently selected on the Subjects tab of the Resources pane and in the 3D Perspective view.

Filter Trajectories - VCM Spline

Vicon Gait Model event VCM Spline Filter

Filter Trajectories - Woltring

Filters the data using the Woltring filter to ensure smooth trajectories for calculating kinetics.

Delete Optional Subject Marker

Run on a any trial to delete a specified group of subject markers from the marker list that will not be used during the dynamic captures.

Delete Unlabeled Trajectories

Run on a fully labeled trial to delete any remaining unlabeled trajectories. Includes the option to choose maximum length of unlabeled trajectory to delete.


Data Processing operations

Use Processing operations to automate real-time and offline motion capture data processing.

Operation

Description

Process Static Plug-in Gait Model

Runs the static Plug-In Gait model on the active subject of the current trial.

For more information, see Modeling with Plug-in Gait in the Vicon Nexus User Guide and the Plug-in Gait Reference Guide.

Calculate Gait Cycle Parameters

Calculate Vicon Gait Model temporal parameters. Includes the option to set the output units.

Process Dynamic Plug-in Gait Model

Runs the dynamic Plug-In Gait model on the active subject of the current trial.
For more information, see Modeling with Plug-in Gait in the Vicon Nexus User Guide and the Plug-in Gait Reference Guide.

Run Static BodyLanguage Model

Runs the static BodyLanguage model

Run Static Oxford Foot Model

Runs the static Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.

Run Dynamic BodyLanguage Model

Runs the dynamic BodyLanguage model

Run Dynamic Oxford Foot Model

Runs the dynamic Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.

Run MatLab Operation

Execute MATLAB script.

For information on using MATLAB with Nexus, see Modeling with MATLAB.

Run ProCalc Operation

Run ProCalc scripts/models directly from Nexus.

For information on Procalc, see the Vicon Procalc documentation.

Run Python Operation

Execute Python script.

For information on using Python with Nexus, see Modeling with Python.

Process OCST

Finds the coordinate system trace using the Optimum Common Shape Technique.

For more information, see Biomechanics workflow.

Process SCoRE / SARA

Generates joint position model outputs using Symmetrical Center of Rotation Estimation and Symmetrical Axis of Rotation Analysis.

For more information, see Biomechanics workflow.

Calculate Gait Deviation Index

Generates a GDI (Gait Deviation Index) score for the subject of the current trial.1

When you run this operation on a trial, two GDI values (left and right), are output to the log and saved as subject parameters. 

To output these values when you run the Export ASCII pipeline operation, select the Export Gait Cycle Parameters option.

Delete Model Outputs

Enables you to delete from the current trial the selected model output(s), all model outputs, or to specify a comma-separated list of model output names.
Tip: You can also access the same options by right-clicking the relevant node in the Subjects Resources tree.

  1. The following research publication provides supporting information on the scientific basis and validation of Vicon's implementation of the calculation of the GDI score:
    SCHWARTZ, M. H., and ROZUMALSKI, A., The gait deviation index: A new comprehensive index of gait pathology, Gait & Posture 28 (2008), p351–357.

File Export operations

Use File Export operations to export of data from Vicon Nexus for use with third-party software packages.

Operation

Description

Export 3D Overlay Video

Export a copy of the reference video .avi file(s) with the 3D Perspective data overlaid onto the video image. You can choose which 3D view option to display and select the codec used to compress the new .avi file.

You can configure the following settings in the Properties section:

  • View Options Set The .options configuration files that have been saved in the Options dialog box (F7). You can select settings for the 3D data to be exported with the .avi file. Select a configuration file from the drop-down list. If you do not specify a file, the current view options are used.
    Default: blank
  • Video Codec The video compression method to use when exporting the .avi file. Select a codec appropriate for the digital camera used to capture the .avi file.
    Default: (None)
  • First Frame and Last Frame Enables you to specify the range of frames to export.

Tip: If you want to export labeled subjects in the Nexus 3D workspace, use instead the Export Workspace to AVI button (available on the View pane toolbar) . For more information, see Export 3D Workspace as AVI in the Vicon Nexus User Guide.

Export ASCII

Export delimited ASCII format to a .csv or .txt file, or another format that you specify by clearing the Macro check box (click the downward arrow at the right of the extension list) and entering the required extension. You can select commas, tabs, or line feeds as the delimiter.

Export C3D

Export the current state of the processed data to a .c3d file. You can then import the data into other software for further processing or report generation. For example, in Vicon Polygon you can visualize the trajectories, kinematic model elements, and kinetics data.

If you manually import the corresponding .vst file into Polygon, it also visualizes the bones.

Export MKR

Export an .mkr file. You can choose whether the exported file name is based on the active subject name(s) or active labeling skeleton template name(s). If you choose Active Labeling Skeleton Names, the name of any labeling skeleton template attached to the subject (for example, PlugInGait FullBody Ai) is used as the name of the MKR file. If more than one subject is present with the same model attached, a log message indicates that only one MKR file will be exported.

Export MOX

Export Nexus data files in .mox format for MoXie
(http://moxie.smalll.eu/).

Export MP

Export the current subject parameters to an .mp file (subject parameter file compatible with legacy software).

Export TRC

Export a .trc file.

Export VSK

Export a labeling skeleton (.vsk) file

Export XCP

Export the current calibration file to an .xcp file in a specified location.

Export MOTExport files in .mot format for use in OpenSim.

Save Trial - C3D + VSK

Save the files associated with the currently open trial.


For more information on how to use the export operations, see Export trial data in the Vicon Nexus User Guide.

System operations

Use System operations to automate oflline camera calibration and applying codecs to video files.

Operation

Description

Process Offline Camera Calibration

Run on a captured trial of a calibration wand wave to calibrate a system (instead of calibrating the system live).

Transcode Video for Trial

Automates transcoding the raw video files associated with the current trial. Enables you to choose the required codec.

Apply Codec to Video

Applies a codec to all AVIs associated with the current trial. You can select which codec to use, whether to keep the original movie file, and whether to remove interlacing.

Important: Reverting to the backup file to re-do the de-interlacing is not supported in Nexus. For more information, see De-interlace AVI files in the Vicon Nexus User Guide.

Reset force plate offsets

Resets the force plate offsets. Enables you to specify the range of frames on which to operate, the affected device(s), and the range of frames to use for zeroing the force plate.

Set Camera Calibration Origin

Sets the camera calibration origin using a calibration object.

Legacy operations

Use Legacy operations to automate the processing of legacy trial data:  

Operation

Description

Nexus Legacy Labeler

Run on fully reconstructed trials to label the subject as a whole instead of frame-by-frame as in the Core Processor. This operation requires a .vsk file.

Nexus Legacy Fit Motion

Run on fully labeled trials to Kinematic Fit the trial as a whole instead of frame-by-frame as in the Core Processor.